Contacts of the helix formed by residues 58 - 69 (chain B) in PDB entry 3E17
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A SER* 5.7 0.9 - - - -
58A SER* 4.1 29.8 - - - +
21B SER* 5.3 0.4 - - - -
23B ILE* 4.2 0.2 - - - -
56B ASN 3.7 2.4 + - - -
57B MET* 1.3 80.0 - - - +
59B LEU* 1.3 58.2 + - - +
60B THR* 3.7 8.6 + - - -
61B ASP* 3.1 31.7 + - - +
62B ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 39.7 - - + +
20A GLY* 3.8 9.6 - - - +
21A SER* 4.2 15.2 + - - +
56A ASN* 3.3 49.3 + - + +
57A MET 6.2 0.2 - - - -
58A SER* 5.8 0.6 - - - +
23B ILE* 4.0 11.5 - - + +
57B MET 3.6 1.8 + - - -
58B SER* 1.3 71.5 - - - +
60B THR* 1.3 58.9 + - - +
62B ALA* 3.2 0.9 + - + +
63B ARG* 2.9 70.1 + - + +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B SER* 3.2 8.9 + - - -
59B LEU* 1.3 79.5 - - - +
61B ASP* 1.3 63.4 + - - +
63B ARG* 3.4 10.7 + - - +
64B LYS* 3.1 49.1 + - - +
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B MET* 3.6 19.7 - - + +
58B SER* 3.1 26.9 + - - +
60B THR* 1.3 75.0 - - - +
62B ALA* 1.3 65.7 + - - +
64B LYS* 3.3 28.8 + - - +
65B LEU* 3.2 23.4 + - - +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.4 11.0 - - + -
23B ILE* 3.8 28.3 - - + -
49B ILE* 3.9 16.3 - - + +
57B MET* 3.5 15.5 - - - -
58B SER 2.9 19.1 + - - +
59B LEU* 3.7 4.5 - - + +
61B ASP* 1.3 72.5 - - - +
63B ARG* 1.3 62.1 + - - +
65B LEU* 3.1 14.5 + - - +
66B ILE* 3.2 15.6 + - - +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.2 17.2 - - - +
19A LEU* 3.1 34.9 + - + +
56A ASN* 5.1 4.0 - - - +
59B LEU* 2.9 53.6 + - + +
60B THR* 3.7 8.2 + - - +
62B ALA* 1.3 72.5 - - - +
64B LYS* 1.3 67.0 + - + +
66B ILE* 3.2 10.2 + - + +
67B GLU* 3.0 27.6 + - + +
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B THR* 3.1 36.4 + - - +
61B ASP* 3.5 25.6 + - - +
62B ALA 3.3 0.4 - - - -
63B ARG* 1.3 76.8 - - - +
65B LEU* 1.3 55.7 + - + +
67B GLU* 3.3 10.0 + - - +
68B LYS* 2.9 28.7 + - - +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 4.0 32.8 - - + +
50B ASN* 4.7 4.7 - - + +
52B THR* 3.8 35.2 - - + +
54B THR* 4.7 2.0 - - + -
57B MET* 3.7 30.3 - - + -
61B ASP 3.2 11.1 + - - +
62B ALA* 3.1 9.7 + - - +
64B LYS* 1.3 76.2 - - - +
66B ILE* 1.3 60.5 + - - +
68B LYS* 3.2 25.2 + - + +
69B SER* 3.2 21.0 + - - -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.9 29.4 - - + -
17A LEU* 4.3 22.2 - - + +
19A LEU* 3.3 35.7 - - + -
49B ILE* 4.3 12.3 - - + -
62B ALA 3.2 12.3 + - - +
63B ARG* 3.2 10.6 + - - +
65B LEU* 1.3 72.8 - - - +
67B GLU* 1.3 66.0 + - - +
69B SER* 2.6 27.8 + - - -
73B LEU* 4.3 18.2 - - + -
75B LEU* 5.5 1.1 - - + -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LYS* 5.8 1.6 + - - -
63B ARG* 3.0 21.6 + - + +
64B LYS* 3.3 8.9 + - - +
66B ILE* 1.3 82.0 - - - +
68B LYS* 1.3 60.2 + - - +
69B SER* 3.5 0.9 + - - -
70B ARG* 4.0 6.6 + - - -
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LYS 2.9 16.5 + - - +
65B LEU* 3.4 26.5 - - + +
66B ILE 3.1 0.6 - - - -
67B GLU* 1.3 72.7 - - - +
69B SER* 1.3 60.9 + - - +
70B ARG* 3.1 12.5 + - - +
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 2.8 25.0 + - - -
50B ASN* 3.3 19.2 - - - +
65B LEU 3.2 6.0 + - - -
66B ILE 2.6 21.0 + - - -
68B LYS* 1.3 76.0 - - - +
70B ARG* 1.3 69.7 + - - +
71B GLY 3.8 0.5 + - - -
72B LYS* 3.1 32.4 + - - +
73B LEU* 4.0 10.5 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il